a) If the encoding is wrong, how is it changed? This is on the book info interface.
b) How to get a different font?
c) In general, how to get to the preferences interface?
d) How to use FBReader for HTML and MOBI, and how to use FBReader for only some MOBIs (i.e. the DRM-free ones)?

Assuming the book info and tools (preferences) interfaces are still there, the above are mostly a problem because of the lack of hardware keys. So perhaps they could be worked around using the on-screen keyboard. I would certainly use FBReader for HTML and MOBI if given the choice, ditching the MobiPocket Reader.

My other concern is that I like FBReader's library, which is a huge improvement over the contentlister, but I can live with no library if I can customize FBReader otherwise. Certainly, a usable full screen mode and faster page turns will be a big help.

The options page is still intact. But using it would be troublesome because there are no screen refreshes programmed in. Your best bet would be to install dropbear, ssh into the iLiad, modify /mnt/settings/.FBReader/options.xml and map two of the keys to the options and book info dialog. You may also want to either manually call displayMgrClient from the shell to refresh the display, or modify the launching script to use the hacked libX11.

As my time lately has grown increasingly scarce, I decided to use this method to speed along porting time. I'll upload my sources if someone wants to work on a more featured port.